Electrochemical Aptamer-Based Sensors for Rapid Point-of-Use Monitoring of the Mycotoxin Ochratoxin A Directly in a Food Stream.

The ability to measure the concentration of specific small molecules continuously and in real-time in complex sample streams would impact many areas of agriculture, food safety, and food production. Monitoring for mycotoxin taint in real time during food processing, for example, could improve public health. Towards this end, we describe here an inexpensive electrochemical DNA-based sensor that supports real-time monitor of the mycotoxin ochratoxin A in a flowing stream of foodstuffs

Predictions of structural elements for the binding of Hin recombinase with the hix site of DNA

Molecular dynamics simulations were coupled with experimental data from biochemistry and genetics to generate a theoretical structure for the binding domain of Hin recombinase complexed with the hix site of DNA. The theoretical model explains the observed sequence specificity of Hin recombinase and leads to a number of testable predictions concerning altered sequence selectivity for various mutants of protein and DNA. Combining molecular dynamics simulations with constraints based on current knowledge of protein structure leads to a theoretical structure of the binding domain of Hin recombinase with the hix site of DNA. The model offers a mechanistic explanation of the presently known characteristics of Hin and predicts the effects of specific mutations of both protein and DNA. The predictions can be tested by currently feasible experiments that should lead to refinements in and improvements on the current theoretical model. Because current experimental and theoretical methods are all limited to providing only partial information about protein-DNA interactions, we believe that this approach of basing molecular simulations on experimental knowledge and using the results of these simulations to design new, more precise experimental tests will be of general utility. These results provide additional evidence for the generality of the helix-turn-helix motif in DNA recognition and stabilization of proteins on DNA

Linear, redox modified DNA probes as electrochemical DNA sensors

We show here that hybridization-linked changes in the dynamics of a redox-modified, electrode-bound linear (as opposed to stem-loop) probe DNA produce large changes in Faradaic current, allowing for the ready detection of target oligonucleotides

On the rational design of cooperative receptors

Cooperativity (homotropic allostery) is the primary mechanism by which evolution steepens the binding curves of biomolecular receptors to produce more responsive input-output behavior in biomolecular systems. Motivated by the ubiquity with which nature employs this effect, over the past 15 years we, together with other groups, have engineered this mechanism into several otherwise noncooperative receptors. These efforts largely aimed to improve the utility of such receptors in artificial biotechnologies, such as synthetic biology and biosensors, but they have also provided the first quantitative, experimental tests of longstanding ideas about the mechanisms underlying cooperativity. In this article, we review the literature on the design of this effect, paying particular attention to the design strategies involved, the extent to which each can be rationally applied to (and optimized for) new receptors, and what each teaches us about the origins and optimization of this important phenomenon

α,ω-Dithiol Oligo(phenylene vinylene)s for the Preparation of High-Quality π-Conjugated Self-Assembled Monolayers and Nanoparticle-Functionalized Electrodes

While thioacetate-terminated oligo(phenylene vinylene)s (OPVs) have been synthesized and employed in applications involving the formation of metal–molecule–metal junctions, the synthesis and application of potentially more versatile α,ω-dithiol OPVs have not previously been described. Here, a thiomethyl-precursor route to the synthesis of α,ω-dithiol OPVs is reported and their ability to form well-ordered self-assembled monolayers (SAMs) without the addition of exogenous deprotection reagents is described. α,ω-Dithiol OPV monolayers exhibit thicknesses consistent with molecular length and are nearly defect-free, as assayed by electrochemical measurements. To demonstrate the ease with which SAMs containing these bifunctional OPVs can, in contrast to thioacetate functionalized OPVs, be further functionalized with materials other than gold, we have modified them in a single step with a sub-monolayer of cadmium selenide nanocrystals (NCs). Scanning electron microscopy (SEM) and atomic force microscopy (AFM) confirm that these NC-modified films are both smooth and uniform over the largest areas investigated (\u3e 10 μm2) and no evidence of NC aggregation is observed. To evaluate the electrochemical response of these metal–molecule– semiconductor assemblies we have fabricated NC-modified OPV SAMs with ferrocene-coated NCs. Variable-frequency alternating current voltammetry indicates that electron transfer in these assemblies is much more rapid than in analogous structures formed using simple alkane dithiols. It thus appears that α,ω-dithiol OPVs are well suited for the formation of high-quality conducting SAMs for the functionalization of gold and other surfaces

α,ω-Dithiol Oligo(phenylene vinylene)s for the Preparation of High-Quality π-Conjugated Self-Assembled Monolayers and Nanoparticle-Functionalized Electrodes

While thioacetate-terminated oligo(phenylene vinylene)s (OPVs) have been synthesized and employed in applications involving the formation of metal–molecule–metal junctions, the synthesis and application of potentially more versatile α,ω-dithiol OPVs have not previously been described. Here, a thiomethyl-precursor route to the synthesis of α,ω-dithiol OPVs is reported and their ability to form well-ordered self-assembled monolayers (SAMs) without the addition of exogenous deprotection reagents is described. α,ω-Dithiol OPV monolayers exhibit thicknesses consistent with molecular length and are nearly defect-free, as assayed by electrochemical measurements. To demonstrate the ease with which SAMs containing these bifunctional OPVs can, in contrast to thioacetate functionalized OPVs, be further functionalized with materials other than gold, we have modified them in a single step with a sub-monolayer of cadmium selenide nanocrystals (NCs). Scanning electron microscopy (SEM) and atomic force microscopy (AFM) confirm that these NC-modified films are both smooth and uniform over the largest areas investigated (\u3e 10 μm2) and no evidence of NC aggregation is observed. To evaluate the electrochemical response of these metal–molecule– semiconductor assemblies we have fabricated NC-modified OPV SAMs with ferrocene-coated NCs. Variable-frequency alternating current voltammetry indicates that electron transfer in these assemblies is much more rapid than in analogous structures formed using simple alkane dithiols. It thus appears that α,ω-dithiol OPVs are well suited for the formation of high-quality conducting SAMs for the functionalization of gold and other surfaces

Activity modulation and allosteric control of a scaffolded DNAzyme using a dynamic DNA nanostructure.

Recognition of the fundamental importance of allosteric regulation in biology dates back to not long after its discovery in the 1960s. Our ability to rationally engineer this potentially useful property into normally non-allosteric catalysts, however, remains limited. In response we report a DNA nanotechnology-enabled approach for introducing allostery into catalytic nucleic acids. Specifically, we have grafted one or two copies of a peroxidase-like DNAzyme, hemin-bound G-quadruplex (hemin-G), onto a DNA tetrahedral nanostructure in such a manner as to cause them to interact, modulating their catalytic activity. We achieve allosteric regulation of these catalysts by incorporating dynamically responsive oligonucleotides that respond to specific "effector" molecules (complementary oligonucleotides or small molecules), altering the spacing between the catalytic sites and thus regulating their activity. This designable approach thus enables subtle allosteric modulation in DNAzymes that is potentially of use for nanomedicine and nanomachines

Effect of Molecular Crowding on the Response of an Electrochemical DNA Sensor

E-DNA sensors, the electrochemical equivalent of molecular beacons, appear to be a promising means of detecting oligonucleotides. E-DNA sensors are comprised of a redox-modified (here, methylene blue or ferrocene) DNA stemloop covalently attached to an interrogating electrode. Because E-DNA signaling arises due to binding-induced changes in the conformation of the stem-loop probe, it is likely sensitive to the nature of the molecular packing on the electrode surface. Here we detail the effects of probe density, target length, and other aspects of molecular crowding on the signaling properties, specificity, and response time of a model E-DNA sensor.Wefind that the highest signal suppression is obtained at the highest probe densities investigated, and that greater suppression is observed with longer and bulkier targets. In contrast, sensor equilibration time slows monotonically with increasing probe density, and the specificity of hybridization is not significantly affected. In addition to providing insight into the optimization of electrochemical DNA sensors, these results suggest that E-DNA signaling arises due to hybridization-linked changes in the rate, and thus efficiency, with which the redox moiety collides with the electrode and transfers electrons

Non-natural protein-protein communication mediated by a DNA-based, antibody-responsive device

We report here the rational design and optimization of an antibody responsive, DNA-based device that enables communication between pairs of otherwise non-interacting proteins. The device is designed to recognize and bind a specific antibody and, in response, undergo a conformational change that leads to the release of a DNA strand, termed the “translator,” that regulates the activity of a downstream target protein. As proof of principle, we demonstrate antibody-induced control of the proteins thrombin and Taq DNA polymerase. The resulting strategy is versatile and, in principle, can be easily adapted to control artificial protein-protein communication in artificial regulatory networks